xcmsPapply: _Deprecated_: xcmsPapply

In yclement/xcms: LC-MS and GC-MS Data Analysis

Description

This function is deprecated, use bplapply instead.

An apply-like function which uses Rmpi to distribute the processing evenly across a cluster. Will use a non-MPI version if distributed processing is not available.

Usage

    xcmsPapply(arg_sets, papply_action, papply_commondata = list(),
           show_errors = TRUE, do_trace = FALSE, also_trace = c())

Arguments

arg_sets	a list, where each item will be given as an argument to papply\_action
papply_action	A function which takes one argument. It will be called on each element of arg\_sets
papply_commondata	A list containing the names and values of variables to be accessible to the papply\_action. 'attach' is used locally to import this list.
show_errors	If set to TRUE, overrides Rmpi's default, and messages for errors which occur in R slaves are produced.
do_trace	If set to TRUE, causes the papply\_action function to be traced. i.e. Each statement is output before it is executed by the slaves.
also_trace	If supplied an array of function names, as strings, tracing will also occur for the specified functions.

Details

Similar to apply and lapply, applies a function to all items of a list, and returns a list with the corresponding results.

Uses Rmpi to implement a pull idiom in order to distribute the processing evenly across a cluster. If Rmpi is not available, or there are no slaves, implements this as a non-parallel algorithm.

xcmsPapply is a modified version of the papply function from package papply 0.2 (Duane Currie). Parts of the slave function were wrapped in try() to make it failsafe and progress output was added.

Value

A list of return values from papply\_action. Each value corresponds to the element of arg\_sets used as a parameter to papply\_action

Note

Does not support distributing recursive calls in parallel. If papply is used inside papply\_action, it will call a non-parallel version

Author(s)

Duane Currie <[e-mail]>, modified by Ralf Tautenhahn <[e-mail]>.

Examples

## Not run: 
library(Rmpi)
library(xcms)

number_lists <- list(1:10,4:40,2:27)

mpi.spawn.Rslaves(nslaves=2)

results <- xcmsPapply(number_lists,sum)
results

mpi.close.Rslaves()


## End(Not run)

yclement/xcms documentation built on April 10, 2020, 12:08 a.m.